Is CC2D1A p.Pro313fs (c.938del) pathogenic?

CC2D1A p.Pro313fs (c.938del) is classified Pathogenic in CC2D1A (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-14). No gnomAD frequency available for this variant.

How common is CC2D1A p.Pro313fs (c.938del) in the general population?

CC2D1A p.Pro313fs (c.938del) is no gnomAD frequency available for this variant (gnomAD).

CC2D1A p.Pro313fs

c.938del · rs750222217 · VCV2836963

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 8 of 29
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.4	GERP -0.017, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CC2D1A
Protein: p.Pro313fs
Coding: c.938del
MANE Select: NM_017721
dbSNP: rs750222217
Type: Deletion
Location: chr19:13918564 (GRCh38)
Gene constraint: LOEUF 0.649 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.71 · 1 PDB
Residue 313: the 'disordered' region

Full CC2D1A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CC2D1A c.511_513+1del Likely pathogenic ★★ same type
CC2D1A p.Gly898fs Pathogenic/Likely pathogenic ★★ same type
CC2D1A p.Lys116fs Pathogenic ★★ same type
CC2D1A c.1222+15_1222+29del Benign/Likely benign ★★ same type
CC2D1A c.2316+21del Likely benign ★★ same type
CC2D1A c.1940+2_1940+5del Likely pathogenic ★ same type
CC2D1A c.49_60+23del Likely pathogenic ★ same type
CC2D1A p.Glu379fs Likely pathogenic ★ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cc2d1a-p-pro313fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown